The gene expression arrays that provide estimates of mRNA levels in tumors have given rise to exon-specific arrays that can identify both gene expression levels, alternative splicing events and mRNA processing alterations. Oligonucleotide arrays are also being used to interrogate single nucleotide polymorphisms (SNPs) throughout the genome for linkage and association studies, and these have been adapted to quantify copy number abnormalities and loss of heterozygosity events. To identify as yet unknown transcripts, tiling arrays across the genome have been developed. Global DNA methylation changes can be detected using array platforms. Additionally it has now become possible to identify DNA-protein interactions using ChIP-on-Chip protocols. With all of these capabilities becoming routine in genomics laboratories, the idea of a systematic characterization of the sum genetic events that give rise to a cancer cell is rapidly becoming a reality.
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